Bolton will start next season in Sky Bet League One with a 12-point deduction after going into administration, the English Football League has announced.
Wanderers, who finished second bottom in the Championship this season, announced earlier on Monday that they had appointed Paul Appleton and Asher Miller of David Rubin and Partners as the club's joint administrators.
"The EFL can confirm that it has been formally notified that administrators have been appointed in respect of Bolton Wanderers Football Club," read an EFL statement.
"As a result, the club is now subject to a 12-point deduction and, in accordance with EFL Regulations, the sporting sanction will take effect next season in League One.
"The EFL will now commence discussions with the administrators with the aim of achieving a long-term future for the club."
Wanderers filed their notice of intention to appoint administrators last week after a recent winding-up order was adjourned at an Insolvency and Companies Court hearing in London.
"The decision was finally made for the appointments which it is hoped will ensure the continued existence of the club, one of the founding members of the Football League," Bolton said in a statement on their official website.
"It has got to the stage where the Trust could not sit back and allow the club to go into liquidation. Decisive action had to be taken and the Trust believes the decision is in the best interests of Bolton Wanderers."
Bolton owe the taxman over £1m, while a proposed takeover by former Watford owner Laurence Bassini fell through.
Wanderers chairman Ken Anderson confirmed last week he had been left with no choice other than to place the club in administration after Bassini failed to provide proof of funding.
Appleton said: "This has obviously been a long-running situation and it is vitally important that we quickly establish the position of both the football club and the holding company.
"Everybody at the club, as well as the supporters, need a sense of clarity and that is what I will be seeking to provide as quickly as possible."
Bolton, relegated to League One, were granted a second stay of execution by the High Court earlier this month.
Wanderers faced a winding-up petition on 3 April over an unpaid tax bill but the case was adjourned until May 8 to allow the proposed sale of the club to proceed.
That was then put on hold after the club informed the court they would be appointing administrators.
It was the sixth time in the last 18 months that Bolton have faced a winding-up order. The latest one was issued in February by HMRC over debts of £1.2m.
The cash-strapped club were unable to fulfil their final home league game of the season against Brentford after the players went on strike in protest at unpaid wages.
Bolton Council's Safety Advisory Group issued a prohibition notice preventing the rearranged fixture from taking place and the EFL announced it would not be played at a future date.
Brentford were awarded three points on the basis of a 1-0 win, which moved them up from 15th to 12th in the table.
The EFL said Bolton were guilty of misconduct and that there would be disciplinary proceedings taken against them.